Hi,<div>I am doing on hacking gromacs and, since gromacs code is very complicated, </div><div>in my opinion it is better avoiding to touch so deeply the code.<div><br></div><div>You can do simply writing your own function and executing it after (or before, it depends by the details of your modification)</div>
<div>do_force (in md.c) simply modifying the f vector and printing the output after print_ebin (the function that actually prints results). </div><div>Of course this approach is right just if your modification can be developed as an independent module.</div>
<div><br></div><div>Regarding coordinates, because of domain decomposition, each node can access only to local atom data.</div><div><br></div><div>To obtain the local index starting from the global index, you need to execute the following code (tested on gromacs 4.5.5):</div>
<div><br></div><div>#include "gmx_ga2la.h"</div><div><br></div><div>int global_index,local_index,cell_id;</div><div>t_commrec *cr;</div><div><br></div><div><div>for(global_index=0;global_index<atom_count; global_index++)</div>
<div> {</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> cell_id = cr->dd->ga2la->laa[global_index].cell;</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> local_index = cr->dd->ga2la->laa[global_index].la;</div>
</div><div><div> </div><div> if(cell_id == 0)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> {</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> //atom global_index is on this node</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span> }</div></div><div> else</div><div><div><div><span class="Apple-tab-span" style="white-space:pre"> </span> {</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> //atom global_index is NOT on this node</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span> }</div></div></div><div> }</div><div><br></div><div>you can get the atom_count (total number of atoms) in md.c using:</div><div>state_global->natoms </div>
<div><br></div><div>I hope I've helped you :)</div><div><br></div><div>Francesco</div><div><br></div><div><br></div><div><div class="gmail_quote">2012/8/31 alex.bjorling <span dir="ltr"><<a href="mailto:alex.bjorling@gmail.com" target="_blank">alex.bjorling@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I'm now in the exact same position as Radhakrishna describes here. After<br>
posting the following, I did some more research and now have ways to get<br>
both energy and force from a complicated operation over all coordinates.<br>
<br>
<a href="http://gromacs.5086.n6.nabble.com/Adding-an-artificial-energy-term-for-structure-refinement-tp5000240.html" target="_blank">http://gromacs.5086.n6.nabble.com/Adding-an-artificial-energy-term-for-structure-refinement-tp5000240.html</a><br>
<br>
Has anyone been successful in making these modifications?<br>
<br>
Best,<br>
Alex<br>
<br>
<br>
<br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco<br>
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